Taxonomic assignment report
| Facility | Hogwarts |
| Analyst | John Doe |
| Analysis started | 2025-04-06 06:13:48 |
| Analysis completed | 2025-04-06 06:13:48 |
| Wall time | 0:0:0 hours |
Sample details
| locus | 16S mitochondrial rRNA gene |
| preliminary_id | Trogoderma |
| taxa_of_interest |
Trogoderma granarium |
| country | Pakistan |
| host | Rice |
| sample_id | VE25-1428_16S |
| Query DNA sequence |
Result overview
Trogoderma granarium
Positive species identification.
Reasoning - Flag 1A:
1 candidate species matched with high stringency (identity ≥ 98.5%).
| Preliminary morphology ID confirmed | True |
|
Flag 7A: Candidate species is consistent with preliminary morphology ID |
|
| Taxa of interest ruled out | False |
|
Flag 2B: Taxon of interest detected Flag 5.1C: The given locus for this taxon is not present in reference database (0 entries) Flag 5.2C: ≤10% of taxon have reference sequence(s) at the given locus |
|
Analyst evaluation
Identification of candidate species
Flag 1A:
Positive species identification
-
Trogoderma granarium
1 candidate species matched with high stringency (identity ≥ 98.5%)
Candidate hits must meet ONE of these criteria:
| Minimum alignment length |
400bp
|
| Minimum query coverage |
85.0%
|
Candidate hits are then classified as follows:
| Classification | Alignment identity | Number of hits | Number of species |
|---|---|---|---|
| STRONG MATCH | ≥ 98.5% | 14 | 1 |
| MODERATE MATCH | ≥ 93.5% | NA | NA |
| NO MATCH | < 93.5% |
Hits per candidate species (top 10 candidates only)
| Species | Hits | Identity | E-value |
|---|---|---|---|
| Trogoderma granarium | 14 | 100.0% | 0.0 |
Analyst evaluation
Taxa of interest
This sections shows the taxa of interest specified by the submitter. Each of these taxa has been cross-referenced against the candidate species to determine if they might match the taxonomic identity of the sample. A blank row indicates a TOI that did not match any candidate species, meaning that it is unlikely that the sample matches that TOI.
| Taxon of interest | Match rank | Match taxon | Match species | Match accession | Match identity |
|---|---|---|---|---|---|
| Trogoderma granarium | species | Trogoderma granarium | Trogoderma granarium | MZ571637 | 1.0 |
See the Database coverage section to see database coverage for taxa of interest.
Reference sequence source diversity
This analysis evaluates how many independent sources have contributed to reference sequences for each candidate species. This provides a measure of confidence in the taxonomic annotation of references sequences. A sequence that has been annotated by multiple independent sources is more likely to have a correct taxonomic annotation.
Analyst evaluation
Independent sources
Flag 4A:
Reference sequences are from diverse sources and therefore likely to be reliable
Reasoning: Matching sequence records for this species are from >5 independent sources
(found 6 sources)
6 Independent Sources
The matching reference sequences for this species have been annotated by 6 independent source(s). A source is considered independent if the author list or publication title is distinct.
Source 1
| Hit accession | Automated | Authors | Title | Journal |
|---|---|---|---|---|
| MZ571637 | False |
Rako,L. Agarwal,A. Semeraro,L. Broadley,A. Rodoni,B.C. Blacket,M.J. |
A LAMP (loop-mediated isothermal amplification) test for rapid identification of Khapra beetle (Trogoderma granarium) | Pest Manag Sci (2021) In press |
| MZ571637 | False |
Blacket,M. Rako,L. Agarwal,A. |
Direct Submission | Submitted (13-JUL-2021) AVR, Agriculture Victoria, AgriBio, Bundoora, Victoria 3083, Australia |
| MZ571636 | False |
Rako,L. Agarwal,A. Semeraro,L. Broadley,A. Rodoni,B.C. Blacket,M.J. |
A LAMP (loop-mediated isothermal amplification) test for rapid identification of Khapra beetle (Trogoderma granarium) | Pest Manag Sci (2021) In press |
| MZ571636 | False |
Blacket,M. Rako,L. Agarwal,A. |
Direct Submission | Submitted (13-JUL-2021) AVR, Agriculture Victoria, AgriBio, Bundoora, Victoria 3083, Australia |
Source 2
| Hit accession | Automated | Authors | Title | Journal |
|---|---|---|---|---|
| KJ930431 | False |
Olson,R.L.O. Farris,R.E. Barr,N.B. Cognato,A.I. |
Molecular identification of Trogoderma granarium (Coleoptera: Dermestidae) using the 16S gene | Unpublished |
| KJ930431 | False |
Olson,R.L.O. Farris,R.E. Barr,N.B. Cognato,A.I. |
Direct Submission | Submitted (02-JUN-2014) Center for Learning Innovation, University of Minnesota, Rochester, 111 South Broadway Suite 300, Rochester, MN 55904, USA |
| KJ930432 | False |
Olson,R.L.O. Farris,R.E. Barr,N.B. Cognato,A.I. |
Molecular identification of Trogoderma granarium (Coleoptera: Dermestidae) using the 16S gene | Unpublished |
| KJ930432 | False |
Olson,R.L.O. Farris,R.E. Barr,N.B. Cognato,A.I. |
Direct Submission | Submitted (02-JUN-2014) Center for Learning Innovation, University of Minnesota, Rochester, 111 South Broadway Suite 300, Rochester, MN 55904, USA |
| KJ930452 | False |
Olson,R.L.O. Farris,R.E. Barr,N.B. Cognato,A.I. |
Molecular identification of Trogoderma granarium (Coleoptera: Dermestidae) using the 16S gene | Unpublished |
| KJ930452 | False |
Olson,R.L.O. Farris,R.E. Barr,N.B. Cognato,A.I. |
Direct Submission | Submitted (02-JUN-2014) Center for Learning Innovation, University of Minnesota, Rochester, 111 South Broadway Suite 300, Rochester, MN 55904, USA |
| KJ930433 | False |
Olson,R.L.O. Farris,R.E. Barr,N.B. Cognato,A.I. |
Molecular identification of Trogoderma granarium (Coleoptera: Dermestidae) using the 16S gene | Unpublished |
| KJ930433 | False |
Olson,R.L.O. Farris,R.E. Barr,N.B. Cognato,A.I. |
Direct Submission | Submitted (02-JUN-2014) Center for Learning Innovation, University of Minnesota, Rochester, 111 South Broadway Suite 300, Rochester, MN 55904, USA |
Source 3
| Hit accession | Automated | Authors | Title | Journal |
|---|---|---|---|---|
| OM388538 | False |
mzhr,N.N. Jawad,M.M. Sabr,A.J. |
Direct Submission | Submitted (25-JAN-2022) biology, Baghdad university, palestine street, baghdad, baghgdad 10046, Iraq |
| OM389182 | False |
mzhr,N.N. Jawad,M.M. Sabr,A.J. |
Direct Submission | Submitted (25-JAN-2022) biology, Baghdad university, palestine street, baghdad, baghgdad 10046, Iraq |
| OM388512 | False |
Mzhr,N.N. Jawad,M.M. Sabr,A.J. |
Direct Submission | Submitted (25-JAN-2022) biology, Baghdad university, palestine street, baghdad, baghgdad 10046, Iraq |
| OM388567 | False |
Mzhr,N.N. Jawad,M.M. Sabr,A.J. |
Direct Submission | Submitted (25-JAN-2022) biology, Baghdad university, palestine street, baghdad, baghgdad 10046, Iraq |
| OM389131 | False |
Mzhr,N.N. Jawad,M.M. Sabr,A.J. |
Direct Submission | Submitted (25-JAN-2022) biology, Baghdad university, palestine street, baghdad, baghgdad 10046, Iraq |
Source 4
| Hit accession | Automated | Authors | Title | Journal |
|---|---|---|---|---|
| LC386208 | False |
Furui,S. Miyanoshita,A. Imamura,T. Minegishi,Y. Kokutani,R. |
Qualitative real-time PCR identification of the khapra beetle, Trogoderma granarium (Coleoptera: Dermestidae) | Appl. Entomol. Zool. (Jpn.) 54, 101-107 (2019) |
| LC386208 | False |
Furui,S. Minegishi,Y. Kokutani,R. |
Direct Submission | Submitted (28-MAY-2018) Contact:Satoshi Furui Food Research Institute, NARO, Food Entomology Laboratory; 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan URL :http://www.naro.affrc.go.jp/english/index.html |
Source 5
| Hit accession | Automated | Authors | Title | Journal |
|---|---|---|---|---|
| ON725093 | False |
Kavallieratos,N.G. Boukouvala,M.C. Lorentha Gidari,D. Di Giuseppe,G. Canale,A. Benelli,G. |
Does cross-mating affect behavioral asymmetries and mating success of Trogoderma granarium strains? | Unpublished |
| ON725093 | False | Di Giuseppe,G. | Direct Submission | Submitted (10-JUN-2022) Department of Biology, University of Pisa, Italy, Via A. Volta, 4, Pisa, PI I-56126, Italy |
Source 6
| Hit accession | Automated | Authors | Title | Journal |
|---|---|---|---|---|
| NC_053875 | False |
Zeng,L. Pang,Y. Feng,S. Wang,Y. Stejskal,V. Aulicky,R. Zhang,S. Li,Z. |
Comparative mitochondrial genomics of five Dermestid beetles (Coleoptera: Dermestidae) and its implications for phylogeny | Genomics (2020) In press |
| NC_053875 | False | Direct Submission | Submitted (25-MAR-2021) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA | |
| NC_053875 | False |
Zeng,L. Pang,Y. Li,Z. |
Direct Submission | Submitted (25-FEB-2020) Department of Entomology, College of Plant Protection, China Agricultural University, Yuanmingyuan West Road 2#, Haidian District, Beijing 100193, China |
Database coverage of target taxa
The target taxa include candidate species, the preliminary morphology ID, and any taxa of interest provided by the submitter. Each of these taxa are independently evaluated against the reference database to determine whether sufficient reference data exists to support identification of the target taxon. Insufficient coverage of a taxon can result in that taxon not be correctly identified as the taxonomic identity of the sample. For example, if the sample is Homo sapiens, but Homo sapiens sequences are not included in the reference database, the analysis will be unable to identity Homo sapiens as the correct taxonomic identity, and will most likely assign the closest relative with reference data as the taxonomic identity.
Analyst evaluation
Database coverage
Flag 5.1C:
The reference database is likely to be unreliable for this species
Reasoning: The given locus for this taxon is not present in reference database (0 entries)
Database coverage of Trogoderma granarium
Flag 5.1C:
The reference database is likely to be unreliable for this species
Reasoning: The given locus for this taxon is not present in reference database (0 entries)
There are 0 sequences in the reference database for Trogoderma granarium at the given locus 16S mitochondrial rRNA gene.
Global occurrence records for Trogoderma granarium.
Note that the occurrence data are not exhaustive, and it is possible for this species to occur in regions not shown on the map.
Database coverage of species in genus Trogoderma
Flag 5.2C:
The database has poor support for species in this genus
Reasoning: ≤10% of taxon have reference sequence(s) at the given locus
/ (%) sequence records were found in the reference database for:
- Species in the genus Trogoderma
- At the target locus 16S mitochondrial rRNA gene
Number of GenBank records at locus 16S mitochondrial rRNA gene
Database coverage of species in genus Trogoderma that occur in country of origin
Flag 5.3C:
Probability that a different related species from the country of origin is the true taxonomic identity: LOW
Reasoning: No species in genus have been observed in the country of origin
/ (%) sequence records were found in the reference database for:
- Species in the genus Trogoderma
- At the target locus 16S mitochondrial rRNA gene
- In the sample country of origin Pakistan
Number of GenBank records at locus 16S mitochondrial rRNA gene
Database coverage
Flag 5.1C:
The reference database is likely to be unreliable for this species
Reasoning: The given locus for this taxon is not present in reference database (0 entries)
Database coverage of Trogoderma
Flag 5.1C:
The reference database is likely to be unreliable for this species
Reasoning: The given locus for this taxon is not present in reference database (0 entries)
There are 0 sequences in the reference database for Trogoderma at the given locus 16S mitochondrial rRNA gene.
Global occurrence records for Trogoderma.
Note that the occurrence data are not exhaustive, and it is possible for this species to occur in regions not shown on the map.
Database coverage of species in genus Trogoderma
Flag 5.2C:
The database has poor support for species in this genus
Reasoning: ≤10% of taxon have reference sequence(s) at the given locus
/ (%) sequence records were found in the reference database for:
- Species in the genus Trogoderma
- At the target locus 16S mitochondrial rRNA gene
Number of GenBank records at locus 16S mitochondrial rRNA gene
Database coverage of species in genus Trogoderma that occur in country of origin
Flag 5.3A:
Probability that a different related species from the country of origin is the true taxonomic identity: LOW
Reasoning: All species in genus from country of origin have reference sequence(s) for this locus
/ (%) sequence records were found in the reference database for:
- Species in the genus Trogoderma
- At the target locus 16S mitochondrial rRNA gene
- In the sample country of origin Pakistan
Number of GenBank records at locus 16S mitochondrial rRNA gene
Database coverage
Flag 5.1C:
The reference database is likely to be unreliable for this species
Reasoning: The given locus for this taxon is not present in reference database (0 entries)
Database coverage of Trogoderma granarium
Flag 5.1C:
The reference database is likely to be unreliable for this species
Reasoning: The given locus for this taxon is not present in reference database (0 entries)
There are 0 sequences in the reference database for Trogoderma granarium at the given locus 16S mitochondrial rRNA gene.
Global occurrence records for Trogoderma granarium.
Note that the occurrence data are not exhaustive, and it is possible for this species to occur in regions not shown on the map.
Database coverage of species in genus Trogoderma
Flag 5.2C:
The database has poor support for species in this genus
Reasoning: ≤10% of taxon have reference sequence(s) at the given locus
/ (%) sequence records were found in the reference database for:
- Species in the genus Trogoderma
- At the target locus 16S mitochondrial rRNA gene
Number of GenBank records at locus 16S mitochondrial rRNA gene
Database coverage of species in genus Trogoderma that occur in country of origin
Flag 5.3C:
Probability that a different related species from the country of origin is the true taxonomic identity: LOW
Reasoning: No species in genus have been observed in the country of origin
/ (%) sequence records were found in the reference database for:
- Species in the genus Trogoderma
- At the target locus 16S mitochondrial rRNA gene
- In the sample country of origin Pakistan
Number of GenBank records at locus 16S mitochondrial rRNA gene
Intraspecies diversity
This section provides a phylogeny of the candidate reference sequences. The analyst can use this to make a subjective observation on how well the reference sequences are able to distinguish between species. If the phylogeny shows distinct clades for each species, we can be confident that the molecular data are capable of distinguishing between those species. However, if the phylogeny shows overlap between species, this reduces the capacity of the molecular data to confidently distinguish between those species. In some cases, we may see the query sequence falling outside of the adjacent species' clades, which indicates that our query species is not represented in the reference database, which could indicate a rare or novel species.
Analyst evaluation
Taxonomy Check
The following resources can be used to ensure that the given taxonomy is legitimate and current.
| Taxa | Database |
|---|---|
| General | GBIF |
| General | ITIS |
| Mealybugs & scale | ScaleNet database |
| Thrips | Thripswiki |
| Spider Mites | Spider Mites Database |
| Psocodea (Barklice, Booklice, and Parasitic Lice) | Psocodea Species File Online |
| Orthoptera | Orthoptera Species File Online |
| Drosophilidae | TaxoDros |
| Diptera |
Catalog of the Diptera of the Australasian and Oceanian Regions
Systema Dipterorum |
| Aphids | Aphid Species File |
| Ants |
AntWeb
AntCat |
| Lepidoptera (butterflies and moths) | The Global Lepidoptera Names Index |
| Gracillariidae (primitive moths) | Global Taxonomic Database of Gracillariidae |
| Pyralidae (pyralid moths) | Global Information System on Pyraloidea |
| Tortricidae (tortrix moths) | Tortricidae Resources on the Net |